Backend rework — structured logging, repository pattern, E2E tests

[VECTORG99]

Backend Rework — 4 Issues

This PR consolidates 4 backend improvements for the Joidy monorepo. All 90 tests pass.

Phase 1: #38 — Distributed Tracing & Structured Logging

All 3 Python services (api, ai-service, worker) now have:

• Contextvars-based correlation ID that propagates through asyncio context
• X-Request-ID header propagation: Worker → API → AI-service
• JSON logging in production, colored human-readable output in dev
• CorrelationLogFilter on both stream and file handlers
• RequestIdMiddleware now wired as outermost middleware (previously was missing from main.py)
• AI-service now has structured logging (was previously relying on uvicorn stderr)

Phase 2: #37 — DI / Repository Pattern

• api/repositories.py — single-file repository layer: BaseRepository[T] generic + 18 domain repositories + FastAPI Depends providers
• Deleted api/services/unit_of_work.py — dead code referencing non-existent classes
• Fixed embedding_service.py — removed SessionLocal() direct creation; trigger_embedding() accepts optional db (background task compatible)
• Migrated 6 of 8 DB-using services to use repositories (goal, gamification, github, skill_tree, tag_graph, personal_streak)
• Incremental — note_service and joidy_vault_writer remain on raw session (compatible either way)

Phase 3: #11 — E2E API Tests

• CI fix: .github/workflows/ci.yml now runs python -m pytest instead of unittest — discovers all 4 previously-skipped router tests
• 26 new E2E tests covering note CRUD lifecycle, tag CRUD + parent/cycle detection, goal CRUD + completion, gamification stats/XP
• 82 tests pass (26 new + 56 existing, including 4 previously undetected router tests)

Phase 4: #12 — Obsidian Sync Integration Tests

• 8 new vault sync tests covering vault write endpoints (daily, objectives, skills) and the Obsidian import flow (create with source_path, find by path, update imported note, rebuild-derived)

Files Changed

Phase	Files	Change
#38	api/middleware/correlation_id.py	NEW
#38	api/middleware/request_id.py	MODIFIED
#38	api/logging_config.py	MODIFIED
#38	api/main.py	MODIFIED
#38	ai-service/logging_config.py	NEW
#38	ai-service/main.py	MODIFIED
#38	worker/logging_config.py	MODIFIED
#38	worker/watchers/vault_watcher.py	MODIFIED
#38	worker/tasks/joidy_daily_writer.py	MODIFIED
#38	api/routers/ai.py	MODIFIED
#37	api/repositories.py	NEW
#37	api/services/embedding_service.py	MODIFIED
#37	api/services/goal_service.py	MODIFIED
#37	api/services/gamification_engine.py	MODIFIED
#37	api/services/github_service.py	MODIFIED
#37	api/services/skill_tree.py	MODIFIED
#37	api/services/tag_graph.py	MODIFIED
#37	api/services/personal_streak_service.py	MODIFIED
#37	api/services/unit_of_work.py	DELETED
#11	.github/workflows/ci.yml	MODIFIED
#11	api/tests/test_e2e_notes.py	NEW
#11	api/tests/test_e2e_tags.py	NEW
#11	api/tests/test_e2e_goals.py	NEW
#11	api/tests/test_e2e_gamification.py	NEW
#12	api/tests/test_e2e_vault.py	NEW

Closes #38, #37, #11, #12